chr6-32358058-C-T

Variant names:

• chr6-32358058-C-T
• rs2894249
• NM_001286474.2:c.218-2389G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286474.2(TSBP1):​c.218-2389G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 152,044 control chromosomes in the GnomAD database, including 45,211 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.77 (45211 hom., cov: 30)
• Consequence: TSBP1 NM_001286474.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 25 publications found

Genes affected

TSBP1 (HGNC:13922): (testis expressed basic protein 1) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

TSBP1-AS1 (HGNC:39756): (TSBP1 and BTNL2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286474.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	NM_001286474.2	MANE Select	c.218-2389G>A		intron	N/A	NP_001273403.1
	TSBP1	NM_006781.5		c.218-2389G>A		intron	N/A	NP_006772.3
	TSBP1	NM_001286475.2		c.197-2389G>A		intron	N/A	NP_001273404.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TSBP1	ENST00000533191.6	TSL:1 MANE Select	c.218-2389G>A		intron	N/A	ENSP00000431199.1
	TSBP1	ENST00000442822.6	TSL:1	c.197-2389G>A		intron	N/A	ENSP00000411164.2
	TSBP1	ENST00000447241.6	TSL:5	c.218-2389G>A		intron	N/A	ENSP00000415517.2

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116784 AN: 151926 Hom.: 45163 Cov.: 30

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.751

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.769 AC: 116888 AN: 152044 Hom.: 45211 Cov.: 30 AF XY: 0.775 AC XY: 57618 AN XY: 74332

African (AFR) AF: 0.715 AC: 29611 AN: 41420

American (AMR) AF: 0.761 AC: 11637 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.791 AC: 2747 AN: 3472

East Asian (EAS) AF: 0.872 AC: 4509 AN: 5168

South Asian (SAS) AF: 0.896 AC: 4301 AN: 4802

European-Finnish (FIN) AF: 0.865 AC: 9168 AN: 10602

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52290 AN: 67980

Other (OTH) AF: 0.754 AC: 1587 AN: 2106

Alfa AF: 0.775 Hom.: 48320

Bravo AF: 0.755

Asia WGS AF: 0.852 AC: 2965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-0.27
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2894249; hg19: chr6-32325835;